Exam 1 Study Guide
Exam 1 Study Guide BIOL-L211 2521
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This 12 page Study Guide was uploaded by AnnaClippinger on Sunday September 20, 2015. The Study Guide belongs to BIOL-L211 2521 at Indiana University taught by Megan Dunn in Summer 2015. Since its upload, it has received 399 views. For similar materials see Molecular Biology in Biology at Indiana University.
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Date Created: 09/20/15
EXAM 1 STUDY GUIDE Key Terms Week 1 Review Session 83115 Molecular Biology the branch of biology that deals with the nature of biological phenomena at the molecular level through the study of DNA and RNA proteins and other macromolecules involved in genetic information and cell function characteristically making use of advanced tools and technologies of separation manipulation imaging and analysis Central Dogma explains the directional flow of genetic information in a cell DNA 9 RNA 9 Protein DNA is transcribed into RNA mRNA and then transcribed into protein Primary Source a type of publication in which scientists describe their own original research studies AUDIENCE specialized fellow scientists within a particular field of study WRITING STYLE technical includes details for other scientists to critique andor duplicate the work COMPONENTS TYPICALLY9 title list of authors abstract introduction materials and methods results including experimental data discussion and references Secondary Source a type of publication that is based on a primary sources commentary on and discussion of the scientific evidence provided in the primary source not as data driven AUDIENCE broad lessspecialized WRITING STYLE general less technical few if any details on methodology or data analysis and is written in a more digestible form COMPONENTS TYPICALLY9 title list of authors text that is not divided into sections introduction materials and methods and such and very few if any citations Genome the entire set of an organisms chromosomes Chromosome a cellular structure consisting of 1 DNA molecule and associated protein molecules A eukaryotic cell typically has multiple linear chromosomes which are located in the nucleus A prokaryotic cell often has a single circular chromosome which is found in the nucleoid a region that is not enclosed by a membrane Somatic Cell diploid 23 pairs of chromosomes 22 pairs of autosomes and 1 pair of sex chromosomes Gamete Cell a haploid reproductive cell such as an egg or sperm Gametes unite during sexual reproduction to produce a diploid zygote Autosome a chromosome that is not directly involved in determining sex not a sex chromosome Sex Chromosome a chromosome responsible for determining sex of an individual Theory of Pangenesis 6th century BC developed by the ancient Greeks and remained current until the 19th century Every part and organ of the body has a pangene BUT they are VERY specific to that organ or body part quotpangenesquot in every organ move throughout the body via the blood and are delivered to the reproductive organs and are then passed on to offspring SO the offspring should have all of the body parts and organs that the parents have and the body parts and organs that are ABSENT in the parents will ALSO be ABSENT in the offspring Germ Plasm Theory works to disprove the Theory ofPangenesis August Weismann 1893 tested if an organism could pass on acquired characteristics to its offspring by cutting the tails off of 2 mice and then mated the mice with no tails and the offspring had tails so he did this for 22 generations and the 23rcl generation still had tails even with 22 generations of ancestors with no tails Hereditary material DOES NOT come from each organ or tissues ONLY germ sperm and egg cells contain hereditary information which is then passed on to offspring GERM CELLS are NOT affected by acquired characteristics and genetic information is NOT passed on by SOMATIC CELLS ONLY GAM ETES Blending Theory 19th century any single inherited trait can only be within the upper and lower values of its 2 parents 9 the offspring of a red and white flower will make pink offspring MAJOR PROBLEM convergence of all variation into 1 9 if this theory were true color variation would be lost in a few generations Gene a segment of DNA that controls an individual trait Locus the physical location of a gene on a chromosome Allele a version of a gene the gene controlling pea shape is either round R or wrinkled r Genotype set of alleles that an individual possesses RR Rr or rr Gets from BOTH parents Phenotype the appearance or manifestation of a feature wrinkled or round Genetic composition vs what you actually see by eye Homozygous possessing 2 of the same alleles of a gene RR or rr Heterozygous possessing 2 different alleles of the same gene Rr Dominant an allele expressed in both homozygotes RR and heterozygotes Rr Usually denoted with an uppercase letter R or with a plus sign r Only the dominant allele is expressed in heterozygotes Recessive an allele whose phenotype is only seen when homozygous rr Usually denoted with a lower case letter r or with a minus sign r NOT expressed 9 only seen when you have 2 of the recessive alleles TrueBreeding referring to organisms that produce offspring of the same variety over many generations of selfpollination Parental Generation P Generation the truebreeding homozygous parent individuals from which F1 hybrid offspring are derived in studies of inheritance F1 Generation the first filial hybrid heterozygous offspring arising from a parental P generation cross F2 Generation the offspring resulting from interbreeding or selfpollination of the hybrid F1 generation TestCross breeding an organism of unknown genotype with a homozygous recessive individual to determine the unknown genotype The ration of phenotypes in the offspring reveals the unknown genotype Dihybrid Cross a cross between 2 organisms that are each heterozygous for both of the characters being followed Punnet Square a diagram used in the study of inheritance to show the predicted genotypic results of random fertilization in genetic crosses between individuals of known genotype Chromosomal Theory of Heredity a basic principle in biology stating that genes are located at specific positions loci in chromosomes and that the behavior of chromosomes during meiosis accounts for inheritance patterns Week 2amp3 Review Session 91415 Homologous Chromosomes a pair of chromosomes of the same length centromere position and staining pattern that possess genes for the same characters at corresponding loci 1 homologous chromosome is inherited from the organism s father the other from the mother Also called a homologous pair NonHomologous Chromosomes chromosomes that are not of the same pair Sister Chromatids 2 copies of a duplicated chromosome attached to each other by proteins at the centromere and sometimes along the arms While joined 2 sister chromatids make up 1 chromosome Chromatids are eventually separated during mitosis or meiosis NonSister Chromatids either of the 2 chromatids of any of the paired homologous chromosomes Linked Genes genes located close enough together on a chromosome that they tend to be inherited together SexLinked Genes a gene located on either sex chromosome Most sexlinked genes are on the X chromosome and show distinctive patterns of inheritance there are very few genes on the Y chromosome Recombination exchange of genetic material between multiple chromosomes or between different regions of the same chromosome MORGAN OBSERVED some combinations of alleles were inherited together at a greater frequency than other combinations ALFRED STU RTEVANT A STUDENT OF MORGAN S genes more closely positioned on a chromosome are more tightly linked together than genes that are farther apart the genes will travel together Synapsis the pairing and physical connection of duplicated homologous chromosomes during prophase of meiosis Crossing Over a form of recombination which occurs during Prophase 1 of Meiosis and only on NON SSTER CHROMATIDS of homologous chromosomes genes that are close together have a higher probability of remaining together during meiosis and does NOT occur during Mitosis Incomplete Dominance the situation in which the phenotype of heterozygotes is intermediate between the phenotypes of individuals homozygous for either allele Codominance the situation in which the phenotypes of both alleles are exhibited in the heterozygote because both alleles affect the phenotype in separate distinguishable ways sometimes NEITHER allele of the same gene is dominant or recessive to the other progeny that are heterozygous for CODOMINANT alleles appear mosaic for BOTH parental phenotypes Transforming Principle Frederick Griffith 1928 used 2 strains for pneumococcal bacteria 9 S strain was pathogenic and the R strain was nonpathogenic When he injected the S strain into a mouse the mouse died and when he injected the R strain into a mouse it lived So he took the S strain and fragmented it with heat and then injected into the mouse and the mouse lived and them mixed the fragmented S strain with the R strain and the mouse died So he concluded that the R strain was transformed by a substance from the heat killed fragmented S strain which became the foundation for later experiments that proved that the transforming substance was DNA Nucleotide the building block of a nucleic acid consisting of a 5carbon sugar covalently bonded to a nitrogenous base and 1 or more phosphate groups consist of a purine or pyrimidine base a sugar deoxyribose in DNA and a phosphate group there are 4 bases within 2 structural classes PURINES Adenine A and Guanine G and PYRIMIDINES Cytosine C and Thymine T nucleotides arejoined together by a phosphodiester bond Purine 1 of 2 types of nitrogenous bases found in nucleotides characterized by a 6membered ring fused to a 5membered ring a structural class of nucleotide bases that consists of Adenine A and Guanine G Pyrimidine 1 of the 2 types of nitrogenous bases found in nucleotides characterized by a 6membered ring a structural class of nucleotide bases that consists of Cytosine C and Thymine T in DNA and Uracil U in RNA The 2 structural classes of the nucleotide bases are paired with each other AT and GC to make the 2 strandschains ANTIPARALLEL and have COMPLEMENTARY SEQUENCES and the bases are bonded together by HYDROGEN BONDS and the hydrogen bonding is important for base specificity AampT have 2 hydrogen bonds while GampC have 3 hydrogen bonds Polymer a long nucleotide consisting of many similar or identical monomers linked together by covalent bonds Phosphodiester Bond in DNA and RNA this bond is the linkage between the 3 carbon atom of 1 sugar molecule and the 5 carbon atom of another deoxyribose is the sugar in DNA and ribose is the sugar in RNA Strong covalent bonds form between the phosphate group and 2 5carbon ring carbohydrates pentoses over 2 ester bonds Antiparallel referring to the arrangement of the sugarphosphate backbones in a DNA double helix they run in opposite 5 9 3 directions Chromatin the complex of DNA and proteins that makes up eukaryotic chromosomes When the cell is not dividing chromatin exists in its dispersed form as a mass of very long thin fibers that are not visible with a light microscope complex of DNA and protein Histone a small protein with a high proportion of positively charged amino acids that binds to the negatively charged DNA and plays a key role in chromatin structure proteins that compact eukaryotic chromosomes absent in prokaryotes FOUR TYPES Nucleosome the basic beadlike unit of DNA packing in eukaryotes consisting of a segment of DNA wound around a protein core composed of 2 copies of each of 4 types of histone unit of DNA wrapped around a protein core composed of 8 histones Gene Density how many genes there are per size RNA Splicing after synthesis of a eukaryotic primary RNA transcript the removal of portions of the transcript introns that will not be included in the mRNA and the joining together of the remaining portions exons ntron noncoding protein regions separate coding exons removed by RNA splicing internal to a coding gene and won t get any structural RNA from it Exon coding regions that will be transcribed and translated Intergenic Region DNA sequences found between genes and do not contain coding sequences or structural RNAs Repetitive Sequences definition for Repetitive DNA nucleotide sequences usually noncoding that are present in many copies in a eukaryotic genome The repeated units may be short and arranged tandemly in series or long and dispersed in the genome 2 general classes Microsatellite short lt13 bp tandem repeats commonly dinucleotide repeats due to errors in copying DNA GenomeWide Repeat large gt100 bp many are gt1 kb can be tandem or dispersed and can be transposable elements aka transposons Transposition the transfer of a DNA segment to a new position on the same or another chromosome Transposon a transposable element a segment of DNA that can move within the genome of a cell by means of a DNA or RNA intermediate that moves within a genome by means of a DNA intermediate mobile genetic element quotjumping genes Composite Transposon contain extra genes between the insertion sequences and is a source of new genetic information for the organism Binary Fission a method of asexual reproduction by quotdivision in half n prokaryotes binary fission does not involve mitosis but in singlecelled eukaryotes that undergo binary fission mitosis is part of the process Mitosis a process pf nuclear division in eukaryotic cells conventionally divided into 5 stages prophase prometaphase metaphase anaphase and telophase Mitosis conserves chromosome number by allocating replicated chromosomes equally to each of the daughter nuclei occurs in somatic cells 2n to Zn want to make identical cells DIVISION OF THE NUCLEUS 2n 2 sets of chromosomes and 1n 1 set of chromosomes Somatic Cell any cell in an organism besides the gametes of chromosomes 46 Zn diploid Gametes egg and sperm of chromosomes 23 1n haploid Meiosis a modified type of cell division in sexually reproducing organisms consisting of 2 rounds of cell division but only 1 round of DNA replication It results in cells with half the number of chromosome sets as the original cell occurs in gametes 2n to 1n 9 to take a diploid set to a haploid set Meiosis the first division of a 2stage process of cell division in sexually reproducing organisms that results in cells with half the number of chromosome sets as the original cell Meiosis the second division of a 2stage process of cell division in sexually reproducing organisms that results in cells with half the number of chromosome sets as the original cell Cell Cycle an ordered sequence of events in the life of a cell from its origin in the division of the parent cell until its own division into 2 The eukaryotic cell cycle is composed of interphase including G1 S and G2 subphases and M phase including mitosis and cytokinesis nterphase a period in the cell cycle when the cell is not dividing During interphase cellular metabolic activity is high chromosomes and organelles are duplicated and cell size may increase nterphase often accounts for about 90 of the cell cycle Cytokinesis the division of the cytoplasm to form 2 separate daughter cells immediately after mitosis meiosis or meiosis Cohesion the linking together of like molecules often by hydrogen bonds Bivalent Attachment during metaphase the mitotic spindle forms and the kinetochores of sister chromatids attach to the microtubules Proper chromatid attachment is only achieved when the 2 kinetochores of a sisterchromatid pair are attached to microtubules emanating from opposite microtubuleorganizing centers This type of attachment is called a bivalent attachment and results in the microtubules exerting tension on the chromatid pair by pulling the sisters in opposite directions Monovalent Attachment attachment of both chromatids to microtubules emanating from the same microtubuleorganizing center or attachment of only 1 chromatid of the pair called a monovalent attachment does not result in tension Core DNA the DNA most tightly associated with the nucleosome Linker DNA the DNA between each nucleosome the string in the quotbeads on a string image HistoneFold Domain a conserved region found in every core histone mediates the assembly of these histone only intermediates without DNA the core histones form intermediate assemblies in solution This is composed of 2 ahelical regions separated by 2 short unstructured loops This domain mediates the formation of the headtotail heterodimers of specific pairs of histones H3 and H4 histones first form heterodimers that then come together to form a tetramer with 2 molecules each of H3 and H4 In contrast H2A and H23 form heterodimers in solution but not tetramers Histone Methyl Transferase HMTs add methyl groups to histones Histone Demethylase HDMs remove methyl groups from histones Histone Acetyltransferase HATs catalyze the addition of acetyl groups to histones Histone Deacetylase HDAcs remove the acetyl groups from histones Methylation has a neutral effect on overall charge of histones and makes histones more hydrophobic and package more tightly in the nucleus which condenses the chromosomes and removing the methyl groups from the histones may promote decondensation Acetylation makes the overall charge of histones more negative may help decondense the chromosomes and the removal of acetyl groups from histones may promote condensation 30 nm Fiber the next level of compaction after the nucleosomes are formed in the higherorder of remodeling chromatin stabilized by histone Nterminal tails and it tightly compacts the nucleosomes NucleosomeRemodeling Complex multiprotein complexes that promote changes in nucleosome location or DNA interaction use the energy released from ATP hydrolysis facilitate 3 types of changes 1 Sliding 2 Ejection 3 Dimer Exchange Week 4 Review Session 92115 SemiConservative Model of Replication favored by Watson and Crick each parental strand serves as a template for newly synthesized DNA Conservative Model of Replication parental strands remain together and the newly synthesized DNA strands are all new strands Dispersive Model of Replication parental strands broken into double stranded fragments used as templates so you get a hybrid molecule Origin of Replication sequence specific positions where replication is initiated multiple origins of replication along the chromosome the site where the replication of a DNA molecule begins consisting of a specific sequence of nucleotides PreReplication Complex preRC complex of proteins that quotmeltquot the double helix creating replication bubbles Replication Fork replication bubbles have 2 replication forks where the bubble starts and stops numerous events occur at or near the replication fork including but not limited to DNA unwound by DNA helicases Primers synthesized by primases and Singlestranded DNA bound by DNA polymerase a Yshaped region on a replicating DNA molecule where the parental strand are being unwound and new strands are being synthesized Helicase unwinds the helical doublestranded DNA at the replication fork an enzyme that untwists the double helix of DNA at replication forks separating the 2 strands and making them available as template strands Primer a short stretch of RNA with a free 3 end bound by complementary base pairing to the template strand and elongated with DNA nucleotides during DNA replication PrimerTemplate Junction primase binds singlestranded DNA adds short 3910 bp primer DNA polymerases can t start synthesis by itselfneeds a 3 hydroxyl to bind and start making new bases The starting point for DNA polymerases to start replication because the primer is added to the template strand of DNA Primase an enzyme that joins RNA nucleotides to make a primer during DNA replication using the parental DNA strand as a template SingleStranded Binding Protein a protein that binds to the unpaired DNA strands during DNA replication stabilizing them and holding them apart while they serve as templates for the synthesis of complementary strands of DNA DNA Polymerase an enzyme that catalyzes the elongation of new DNA by the addition of nucleotides to the 3 end of an existing chain There are several different DNA polymerases DNA polymerase III and DNA polymerase I play major roles in DNA replication in E Coli DNA Polymerase resembles a hand with 3 Domains Palm catalyzes DNA synthesis and monitors base pairing where DNA synthesis actually occurs Fingers bends template strand positions next base to be paired works simultaneously with the palm to keep the DNA moving along Thumb maintains association between DNA polymerase and DNA and makes sure that the DNA strands stay in the palm of the hand Topoisomerase a protein that breaks swivels and rejoins DNA strands During DNA replication topoisomerase helps to relieve strain in the double helix ahead of the replication fork Positive and Negative Supercoiling Positive Supercoils accumulate in front of the replication fork which creates tension and if this knot isn t broken then the replication fork will stop Topoisomerase breaks 1 or both strands to relieve the tensionstrain that the unwinding of doublestranded DNA puts on the unwound DNA at the replication fork holds on to DNA and passes strands through the break and then puts the ends back together which results in Negative Supercoils which is the natural conformation of DNA Leading Strand Synthesis the new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5 9 3 direction Lagging Strand Synthesis a discontinuously synthesized DNA strand that elongates by means of Okazaki fragments each synthesized in a 5 9 3 direction away from the replication fork Sliding Clamp the assembly of multiple subunits binds DNA polymerase form a ring and bind with infinity and to the DNA keeps DNA polymerase from diffusing away from DNA Without a sliding clamp DNA polymerase adds 1015 bases before falling off the template strand With a sliding clamp can add thousands of bases at a time RNase H an endonuclease that removes most of the RNA primer removes the nucleotides internal to DNA Exonuclease proofreads the DNA and removes improperly basepaired dNTPs only removes the most recent errors Holoenzyme physically links 4 enzymes 9 3 DNA Polymerases and 1 sliding clamp loader Replisome all of the proteins acting together at the replication fork Ligase a linking enzyme essential for DNA replication catalyzes the covalent bonding of the 3 end of 1 DNA fragment such as an Okazaki Fragment to the 5 end of another DNA fragment such as a growing DNA chain Telomeres a tandemly repetitive DNA at the end of a eukaryotic chromosome s DNA molecule Telomeres protect the organism s genes from being eroded during successive rounds of replication Telomerase replicates the ends of linear chromosomes and is composed of protein and RNA telomerase binds to the lagging strand and the RNA component extends over the end and serves as a template adds bases that are complementary to own RNA and repeats this process Polymerase Reaction Chain PCR a technique for amplifying DNA in vitro modeled after cellular DNA replication by incubating it with specific primers a heatresistant DNA polymerase and nucleotides Ingredients for PCR DNA Template genomic or plasmid DNA a set of oligonucleotide primers designed to amplify specific region DNA polymerase Modified from quotNormalquot 9 have to use a special DNA Pol that is able to withstand high heat heat stable a solution containing dNTPs and a physiologically relevant salt mixture 3 basic steps plus the end stage 1 Denaturing separate the 2 DNA strands done through heating no replication forks form 2 Annealing attach primers to the DNA strand drop the temperature down to a specific temp to allow the binding of DNA and primers use DNA primers because RNA primers can be contaminated quickly 3 Extension DNA polymerase extends the primer sequence DNA synthesis occurs in continuous stretch 4 Cycle completion of all 3 steps the amount of DNA doubles after each cycle final amount of DNA 2quotx where x of cycles Sanger Sequencing a method of DNA sequencing based on the selective incorporation of chain terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication EXAMPLE reaction with a chainterminating G sometimes normal G added elongating will stop if chainterminating nucleotide is added generates fragments of various lengths which can be separated on gel then repeat for all reactions using the same template each lane a separate reaction with a chainterminating nucleotide fragments separated on gel according to size read from the top to the bottom to deduce the sequence the longest fragment will be at the top and the shortest will be at the bottom Chain Termination this technique utilizes quotchainterminating nucleotides quotnormalquot nucleotide dNTP has 3 OH and quotchainterminating nucleotide ddNTP quotTERMINATES DNA chain has 3 H AGTampC can be made quotchainterminating if there is a quotchainterminating nucleotide at the end of the strand then DNA synthesis will stop ddNTP quotNormal Nucleotide deoxynucleoside triphosphate dNTP dATP dGTP dCTP dTTP 9 the individual dNTPs are added to growing DNA strand based on template strand 3 phosphate groups named alpha a beta 3 and gamma y alpha is closes to the sugar and gamma is farthest away from the sugar phosphodiester bond formation requires removal of B and y phosphates ONLY 0L IN THIS BOND Agarose Gel Electrophoresis method to analyze DNA fragments from PCR or restriction digests uses an electrical charge to separate fragments based on relative size an electric current is applied to the gel and the DNA fragments migrate according to size Anode positive electrode Cathode negative electrode Restriction Endonucleases Restriction Enzyme an endonuclease type of enzyme that recognizes and cuts DNA molecules foreign to a bacterium such as phage genomes The enzyme cuts at specific nucleotide sequences restriction sites Restriction Site a specific sequence on a DNA strand that is recognized and cut by a restriction enzyme Key Points to Focus On The Central Dogma of Biology DNA Transcribed into 9 mRNA Translated into 9 Protein Primary Source vs Secondary Source L2 The different theories of inheritance L2 I Mendelian Genetics I Blending Theory I Germ Plasma Theory I Pangenesis MAKE SURE AND REVIEW THE MOLECULAR BIOLOGY IN THE NEWS ARTICLE The exceptions to Mendelian Genetics L3 I SexLinked Traits Recombination and Genetic Linkage I Incomplete Dominance I Codominance Crossing Over Nonsister chromatids and Prophase I of Meiosis I L3 The DNA as Genetic Material experiments done by L3 I Griffith Transforming Principle I Avery The Transforming Agent is DNA Used Griffith s experiment but used different controls I HersheyChase The Transforming Agent is DNA used a bacteriophage T2 Know the structure of DNA and the different components of a DNA nucleotide L4 I Phosphate group I Sugar Deoxyribose in DNA I Base Purine Adenine Guanine or Pyrimidine Cytosine Thymine Be able to identify each base from a diagram and draw them L4 Transposons and mutagenesis 9 quotJumping Genes 9 Transposase and Repetitive Sequences 9 2 classes Microsatellites and GenomeWide Repeats 9 Composite Transposons 9 Cut and Paste Transposistion L4 Introns and Exons and Noncoding regions and intergenic regions L4 Gene Density amount of genes per size of chromosome Go over Mitosis and Meiosis from BIO 112 Know what a nucleosome is and core DNA DNA most tightly associated with the nucleosome and Linker DNA DNA found between the nucleosomes Cohe on Know the different models of replication The MeselsonStahl experiment KNOW ALL OF THE REPLICATION ENZYMES AND THEIR FUNCTIONS KNOW THE DIRECTION THE LAGGING STRAND AND LEADING STRAND GO WHEN LOOKING AT A DIAGRAM OF A REPLICATION FORK AND ALSO BE ABLE TO DRAW A REPLICATION FORK AND LABEL THE LAGGING AND LEADING STRANDS CORRECTLY Know how telomeres and telomerase help prevent the erosion of chromosomes Know what PCR is and wherewhen it is performed in vitro Be able to sequence a DNA strand from a template strand and the primer 0 Know how to use the Sanger Sequencing Method 0 Know about the agarose gel and how it is used with DNA
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